Statistical modeling of RNA structure profiling experiments enables parsimonious reconstruction of structure landscapes.

RNA plays key regulatory roles in diverse cellular processes, where its functionality often derives from folding into and converting between structures. Many RNAs further rely on co-existence of alternative structures, which govern their response to cellular signals. However, characterizing heterogeneous landscapes is difficult, both experimentally and computationally. Recently, structure profiling experiments have emerged as powerful and affordable structure characterization methods, which improve computational structure prediction. To date, efforts have centered on predicting one optimal structure, with much less progress made on multiple-structure prediction. Here, we report a probabilistic modeling approach that predicts a parsimonious set of co-existing structures and estimates their abundances from structure profiling data. We demonstrate robust landscape reconstruction and quantitative insights into structural dynamics by analyzing numerous data sets. This work establishes a framework for data-directed characterization of structure landscapes to aid experimentalists in performing structure-function studies

Specially Shaped Optical Fiber Probes: Understanding and Their Applications in Integrated Photonics, Sensing, and Microfluidics

Thanks to their capability of transmitting light with low loss, optical fibers have found a wide range of applications in illumination, imaging, and telecommunication. However, since the light guided in a regular optical fiber is well confined in the core and effectively isolated from the environment, the fiber does not allow the interactions between the light and matters around it, which are critical for many sensing and actuation applications. Specially shaped optical fibers endow the guided light in optical fibers with the capability of interacting with the environment by modifying part of the fiber into a special shape, while still preserving the regular fiber’s benefit of low-loss light delivering. However, the existing specially shaped fibers have the following limitations: 1) limited light coupling efficiency between the regular optical fiber and the specially shaped optical fiber, 2) lack special shape designs that can facilitate the light-matter interactions, 3) inadequate material selections for different applications, 4) the existing fabrication setups for the specially shaped fibers have poor accessibility, repeatability, and controllability. The overall goal of this dissertation is to further the fundamental understanding of specially shaped fibers and to develop novel specially shaped fibers for different applications. In addition, the final part of this dissertation work proposed a microfluidic platform that can potentially improve the light-matter interactions of the specially shaped fibers in fluidic environments. The contributions of this dissertation work are summarized as follows: 1) An enhanced fiber tapering system for highly repeatable adiabatic tapered fiber fabrications. An enhanced fiber tapering system based on a novel heat source and an innovative monitoring method have been developed. The novel heat source is a low-cost ceramic housed electric furnace (CHEF). The innovative monitoring method is based on the frequency-domain optical transmission signal from the fiber that is being tapered. The enhanced fiber tapering system can allow highly repeatable fabrication of adiabatically tapered fibers. 2) A lossy mode resonance (LMR) sensor enabled by SnO2 coating on a novel specially shaped fiber design has been developed. The developed LMR sensor has a D-shape fiber tip with SnO2 coating. It has the capability of relative humidity and moisture sensing. The fiber-tip form factor can allow the sensor to be used like a probe and be inserted into/removed from a tight space. 3) Specially shaped tapered fibers with novel designs have been developed for integrated photonic and microfluidic applications. Two novel specially tapered fibers, the tapered fiber loop and the tapered fiber helix have been developed. The tapered fiber loop developed in this work has two superiority that differentiated itself from previous works: a) the mechanical stability of the tapered fiber loop in this work is significantly better. b) the tapered fiber loops in this work can achieve a diameter as small as 15 ?m while still have a high intrinsic optical quality factor of 32,500. The tapered fiber helix developed in this work has a 3D structure that allows it to efficiently deliver light to locations out of the plane defined by its two regular fiber arms. Applications of the tapered fiber helices in both integrated photonic device characterizations and microparticle manipulations have been demonstrated. 4) Developed an acrylic-tape hybrid microfluidic platform that can allow function reconfiguration and optical fiber integration. A low-cost, versatile microfluidic platform based on reconfigurable acrylic-tape hybrid microfluidic devices has been developed. To the best of the author’s knowledge, this is the first time that the fabrication method of sealing the acrylic channel with a reconfigurable functional tape has been demonstrated. The tape-sealing method is compatible with specially shaped fiber integrations

The Design of Heteromeric and Metal-binding Alpha-Helical Barrels

Introduction: The field of protein design has drastically evolved over the past four years. Both the protein folding problem, which involves predicting the 3D arrangement of atoms from a given sequence of amino acids, and its inverse, have been technically solved after 50 years. However, the black box nature of the tools developed to address these problems limits our comprehension of protein folding and dynamics. Harnessing this knowledge could revolutionise sectors such as drug design, disease diagnosis, energy transfer, and material science. This work focuses on the rational design of a protein scaffold called coiled coils, positioning them as a model for advancing our control and understanding of proteins.Results: In this thesis, we navigate the uncharted territory of coiled coils with reduced symmetry. We generate novel A3B3 hexameric α-helical barrels with both parallel and antiparallel helix orientations, expanding understanding of coiled-coil assemblies and introducing new scaffolds. Utilising these assemblies, we create covalently attached bipyridyl functional groups situated within the barrel cores, capable of chelating iron and ruthenium ions. Additionally, we develop intrinsically disordered peptide sequences that assemble only upon the introduction of specific metal ions. This can be applied for both metal sensing, as well as metal mediated sensing of other ligands.Conclusions: This research advances the field of protein design through the generation of novel α-helical barrels and the development of coiled-coil assemblies with innovative functionalities. Our work has allowed for new potential applications in bio-sensing and catalysis and has further demonstrated the broad versatility of coiled-coil scaffolds.Implications: This study illuminates the potential of coiled coils in the understanding of protein structure-function relationships. It introduces metal-sensitive peptide sequences for bio-sensing and photocatalysis within α-helical barrels, potentially paving the way for advancements in applications for de novo designed proteins

GOLLUM: a next-generation simulation tool for electron, thermal and spin transport

We have developed an efficient simulation tool 'GOLLUM' for the computation of electrical, spin and thermal transport characteristics of complex nanostructures. The new multi-scale, multi-terminal tool addresses a number of new challenges and functionalities that have emerged in nanoscale-scale transport over the past few years. To illustrate the flexibility and functionality of GOLLUM, we present a range of demonstrator calculations encompassing charge, spin and thermal transport, corrections to density functional theory such as LDA+U and spectral adjustments, transport in the presence of non-collinear magnetism, the quantum-Hall effect, Kondo and Coulomb blockade effects, finite-voltage transport, multi-terminal transport, quantum pumps, superconducting nanostructures, environmental effects and pulling curves and conductance histograms for mechanically-controlled-break-junction experiments.Comment: 66 journal pages, 57 figure

The role of traction in membrane curvature generation.

Curvature of biological membranes can be generated by a variety of molecular mechanisms including protein scaffolding, compositional heterogeneity, and cytoskeletal forces. These mechanisms have the net effect of generating tractions (force per unit length) on the bilayer that are translated into distinct shapes of the membrane. Here, we demonstrate how the local shape of the membrane can be used to infer the traction acting locally on the membrane. We show that buds and tubes, two common membrane deformations studied in trafficking processes, have different traction distributions along the membrane and that these tractions are specific to the molecular mechanism used to generate these shapes. Furthermore, we show that the magnitude of an axial force applied to the membrane as well as that of an effective line tension can be calculated from these tractions. Finally, we consider the sensitivity of these quantities with respect to uncertainties in material properties and follow with a discussion on sources of uncertainty in membrane shape